Biomolecular network motif counting and discovery by color coding. - Noga Alon; Phuong Dao; Iman Hajirasouliha; Fereydoun Hormozdiari; Süleyman Cenk Sahinalp (ISMB, 2008)

Combinatorial QSAR Modeling of Chemical Toxicants Tested against Tetrahymena pyriformis. - Hao Zhu 012; Alexander Tropsha; Denis Fourches; Alexandre Varnek; Ester Papa; Paola Gramatica; Tomas Öberg; Phuong Dao; Artem Cherkasov; Igor V. Tetko (J. Chem. Inf. Model., 2008)

Quantifying Systemic Evolutionary Changes by Color Coding Confidence-Scored PPI Networks. - Phuong Dao; Alexander Schönhuth; Fereydoun Hormozdiari; Iman Hajirasouliha; Süleyman Cenk Sahinalp; Martin Ester (WABI, 2009)

Inferring cancer subnetwork markers using density-constrained biclustering. - Phuong Dao; Recep Colak; Raheleh Salari; Flavia Moser; Elai Davicioni; Alexander Schönhuth; Martin Ester (Bioinform., 2010)

Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery. - Fereydoun Hormozdiari; Iman Hajirasouliha; Phuong Dao; Faraz Hach; Deniz Yörükoglu; Can Alkan; Evan E. Eichler; Süleyman Cenk Sahinalp (Bioinform., 2010)

PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. - Nancy Y. Yu; James R. Wagner; Matthew R. Laird; Gabor Melli; Sébastien Rey; Raymond Lo; Phuong Dao; Süleyman Cenk Sahinalp; Martin Ester; Leonard J. Foster; Fiona S. L. Brinkman (Bioinform., 2010)

Applicability Domains for Classification Problems: Benchmarking of Distance to Models for Ames Mutagenicity Set. - Iurii Sushko; Sergii Novotarskyi; Robert Körner; Anil Kumar Pandey; Artem Cherkasov; Jiazhong Li; Paola Gramatica; Katja Hansen; Timon Schroeter; Klaus-Robert Müller; Lili Xi; Huanxiang Liu; et al. (J. Chem. Inf. Model., 2010)

Optimally discriminative subnetwork markers predict response to chemotherapy. - Phuong Dao; Kendric Wang; Colin C. Collins; Martin Ester; Anna Lapuk; Süleyman Cenk Sahinalp (Bioinform., 2011)

Assessing the Significance of Data Mining Results on Graphs with Feature Vectors. - Stephan Günnemann; Phuong Dao; Mohsen Jamali; Martin Ester (ICDM, 2012)

CLIIQ: Accurate Comparative Detection and Quantification of Expressed Isoforms in a Population. - Yen-Yi Lin; Phuong Dao; Faraz Hach; Marzieh Bakhshi; Fan Mo; Anna Lapuk; Colin C. Collins; Süleyman Cenk Sahinalp (WABI, 2012)

HIT'nDRIVE: Multi-driver Gene Prioritization Based on Hitting Time. - Raunak Shrestha; Ermin Hodzic; Jake Yeung; Kendric Wang; Thomas Sauerwald; Phuong Dao; Shawn Anderson; Himisha Beltran; Mark A. Rubin; Colin C. Collins; Gholamreza Haffari; Süleyman Cenk Sahinalp (RECOMB, 2014)

ORMAN: Optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms. - Phuong Dao; Ibrahim Numanagic; Yen-Yi Lin; Faraz Hach; Emre Karakoç; Nilgun Donmez; Colin C. Collins; Evan E. Eichler; Süleyman Cenk Sahinalp (Bioinform., 2014)

MEMCover: integrated analysis of mutual exclusivity and functional network reveals dysregulated pathways across multiple cancer types. - Yoo-Ah Kim; Dong-Yeon Cho; Phuong Dao; Teresa M. Przytycka (Bioinform., 2015)

AptaTRACE: Elucidating Sequence-Structure Binding Motifs by Uncovering Selection Trends in HT-SELEX Experiments. - Phuong Dao; Jan Hoinka; Yijie Wang 004; Mayumi Takahashi; Jiehua Zhou; Fabrizio Costa; John Rossi; John Burnett; Rolf Backofen; Teresa M. Przytycka (RECOMB, 2016)

Ups and Downs of Poised RNA Polymerase II in B-Cells. - Phuong Dao; Damian Wójtowicz; Steevenson Nelson; David Levens; Teresa M. Przytycka (PLoS Comput. Biol., 2016)

BeWith: A Between-Within Method for Module Discovery in Cancer using Integrated Analysis of Mutual Exclusivity, Co-occurrence and Functional Interactions (Extended Abstract). - Phuong Dao; Yoo-Ah Kim; Sanna Madan; Roded Sharan; Teresa M. Przytycka (RECOMB, 2017)

BeWith: A Between-Within method to discover relationships between cancer modules via integrated analysis of mutual exclusivity, co-occurrence and functional interactions. - Phuong Dao; Yoo-Ah Kim; Damian Wójtowicz; Sanna Madan; Roded Sharan; Teresa M. Przytycka (PLoS Comput. Biol., 2017)

N-Grammer: Augmenting Transformers with latent n-grams. - Aurko Roy; Rohan Anil; Guangda Lai; Benjamin Lee; Jeffrey Zhao; Shuyuan Zhang 002; Shibo Wang; Ye Zhang; Shen Wu; Rigel Swavely; Tao Yu; Phuong Dao; et al. (CoRR, 2022)